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Background The response of patients with chronic hepatitis B (CHB) to antiviral therapy against hepatitis B virus (HBV) is related to the base line level of HBV DNA, but the mechanism is not clear. The present study aimed to understand the possible relationship between the level of HBV DNA and HBV-specific, nonspecific cytotoxic T lymphocytes (CTL) and natural killer (NK) cells of CHB patients and the mechanism how the HBV DNA level influences the antiviral therapeutic effect.Methods Totally 100 adult patients with CHB who were positive for HBV DNA, HBeAg and (HLA)-A2 were enrolled into this study. HBV DNA was tested by real time fluorescence quantitative polymerase chain reaction (PCR). HBV specific and nonspecific CTL and NK cells were tested by flowcytometry. Serum alanine aminotransferase (ALT) and total bilirubin (Tbil) were determined for each patient using routine biochemical tests. The 100 cases were assigned to two groups based on their HBV DNA level: group A had 48 cases, their HBV DNA level was 104-105 copies/ml, group B had 52 cases, their HBV DNA level was 106-107 copies/ml. HBV specific CTL, nonspecific CTL, NK cells, ALT and Tbil of the two groups were compared.Results HBV DNA level of groups A and B was (4.81±0.39) log10 copies/ml and (6.81±0.40) log10 copies/ml, respectively (t=25.32, P <0.001). HBV specific CTL and NK cells of group A were significantly higher than those of group B (P <0.001 for both). Nonspecific CTL of group A was significantly lower than that of group B (P <0.01). ALT and Tbil of group A were significantly lower than those of group B (P <0.01 and P <0.05, respectively).Conclusions Serum HBV DNA level of patients with CHB is related to HBV specific CTL, nonspecific CTL and NK cells, which might result in inflammatory reaction of liver and cause more damage to liver function. Mechanism of HBV DNA level affecting the efficacy of anti-viral treatment may be related to the levels of HBV specific CTL and NK cells.